# A force field has to be loaded to relax a structure
source leaprc.ff99   # or any other force field

# Load the Tripos mol2 file generated by R.E.D.-III.3
DA = loadmol2 ./Frag-DA.mol2
#
# set the FF atom types to get a correct structure
set DA.1.P type P
set DA.1.O1P type O2
set DA.1.O2P type O2
set DA.1.O5' type OS
set DA.1.O3' type OS
set DA.1.C5' type CT
set DA.1.H5'1 type H1
set DA.1.H5'2 type H1
set DA.1.O4' type OS
set DA.1.C4' type CT
set DA.1.H4' type H1
set DA.1.C3' type CT
set DA.1.H3' type H1
set DA.1.C2' type CT
set DA.1.H2'1 type HC
set DA.1.H2'2 type HC
set DA.1.C1' type CT
set DA.1.H1' type H2
set DA.1.N6 type N2
set DA.1.H61 type H
set DA.1.H62 type H
set DA.1.C6 type CA
set DA.1.C5 type CB
set DA.1.N7 type NB
set DA.1.C8 type CK
set DA.1.H8 type H5
set DA.1.N9 type "N*"
set DA.1.C4 type CB
set DA.1.N3 type NC
set DA.1.C2 type CQ
set DA.1.H2 type H5
set DA.1.N1 type NC
#
# Select the atoms to be relaxed
select DA.1.O5'
select DA.1.P
select DA.1.O1P
select DA.1.O2P
select DA.1.O3'
# 
# relax the atoms selected belonging to the unit DA
relax DA
#
# deselect the atoms previously selected
deselect DA.1
#
# impose a conformation similar to that found in the AMBER force field topology database
impose DA { 1 } {{ O1P P O5' C5' 60.00 }}
impose DA { 1 } {{ P O5' C5' C4' 180.00 }}
# 
# select the center to be flipped
select DA.1.C3'
#
# invert the chirality of the C3' center
flip DA
#
# deselect the atom previously selected
deselect DA.1
#
# select the atoms to be relaxed
select DA.1.O3'
select DA.1.H3'
#
# relax the atoms selected belonging to the unit DA
relax DA
#
# deselect the atom previously selected
deselect DA.1
#
# Save the new set of cartesian coordinates in the Tripos mol2 file format
# (The force field atom types are not conserved to be compatible with R.E.DD.B.)
savemol2 DA ./Frag-DAbis.mol2 0